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I am attempting to establish my sample in the ClearMap2 GUI, but I am running into an error after selecting my source folder, which contains two sub-folders each containing a sequence of tiff files for both the cFos and Autofluorescence channels respectively. We are unfortunately running into the following error log:
files:
[data ] raw : no file
[data ] autofluorescence : no file
[analysis] stitched : no file
[analysis] layout : no file
[analysis] background : no file
[data ] resampled : no file
[data ] autofluorescence_resampled : no file
[data ] resampled_to_autofluorescence : no file
[data ] resampled_aligned_to_autofluorescence: no file
[data ] autofluorescence_to_reference : no file
[data ] autofluorescence_aligned_to_reference: no file
[analysis] cells : no file
[analysis] density : no file
[analysis] tile_extension : no file
Preparing: from source Tif-Source((320, 528, 456),)[uint32]/home/gangliaguardian/anaconda3/envs/ClearMapUi39/...arMap/Resources/Atlas/ABA_25um_2017_annotation.tif
Traceback (most recent call last):
File "/home/gangliaguardian/anaconda3/envs/ClearMapUi39/lib/python3.9/site-packages/ClearMap2-2.1.3-py3.9-linux-x86_64.egg/ClearMap/gui/run_gui.py", line 1133, in load_config_and_setup_ui
tab.setup_workers()
File "/home/gangliaguardian/anaconda3/envs/ClearMapUi39/lib/python3.9/site-packages/ClearMap2-2.1.3-py3.9-linux-x86_64.egg/ClearMap/gui/tabs.py", line 327, in setup_workers
self.wrap_step('Setting up atlas', self.setup_atlas, n_steps=1, save_cfg=False, nested=False) # TODO: abort_func=self.preprocessor.stop_process
File "/home/gangliaguardian/anaconda3/envs/ClearMapUi39/lib/python3.9/site-packages/ClearMap2-2.1.3-py3.9-linux-x86_64.egg/ClearMap/gui/interfaces.py", line 299, in wrap_step
self.main_window.wrap_in_thread(func, *step_args, **step_kw_args)
File "/home/gangliaguardian/anaconda3/envs/ClearMapUi39/lib/python3.9/site-packages/ClearMap2-2.1.3-py3.9-linux-x86_64.egg/ClearMap/gui/run_gui.py", line 629, in wrap_in_thread
return result.get()
File "/home/gangliaguardian/anaconda3/envs/ClearMapUi39/lib/python3.9/multiprocessing/pool.py", line 771, in get
raise self.value
File "/home/gangliaguardian/anaconda3/envs/ClearMapUi39/lib/python3.9/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, **kwds))
File "/home/gangliaguardian/anaconda3/envs/ClearMapUi39/lib/python3.9/site-packages/ClearMap2-2.1.3-py3.9-linux-x86_64.egg/ClearMap/gui/tabs.py", line 406, in setup_atlas
self.preprocessor.setup_atlases()
File "/home/gangliaguardian/anaconda3/envs/ClearMapUi39/lib/python3.9/site-packages/ClearMap2-2.1.3-py3.9-linux-x86_64.egg/ClearMap/processors/sample_preparation.py", line 366, in setup_atlases
res = annotation.prepare_annotation_files(
File "/home/gangliaguardian/anaconda3/envs/ClearMapUi39/lib/python3.9/site-packages/ClearMap2-2.1.3-py3.9-linux-x86_64.egg/ClearMap/Alignment/Annotation.py", line 744, in prepare_annotation_files
data = np.array(s.array)
File "/home/gangliaguardian/anaconda3/envs/ClearMapUi39/lib/python3.9/site-packages/ClearMap2-2.1.3-py3.9-linux-x86_64.egg/ClearMap/IO/TIF.py", line 128, in array
return self.to_clearmap_order(array)
File "/home/gangliaguardian/anaconda3/envs/ClearMapUi39/lib/python3.9/site-packages/ClearMap2-2.1.3-py3.9-linux-x86_64.egg/ClearMap/IO/TIF.py", line 173, in to_clearmap_order
transposed = tif_to_clearmap_order(array, self.axes_order)
File "/home/gangliaguardian/anaconda3/envs/ClearMapUi39/lib/python3.9/site-packages/ClearMap2-2.1.3-py3.9-linux-x86_64.egg/ClearMap/IO/TIF.py", line 66, in axes_order
md = self.metadata(info=['shape'])
File "/home/gangliaguardian/anaconda3/envs/ClearMapUi39/lib/python3.9/site-packages/ClearMap2-2.1.3-py3.9-linux-x86_64.egg/ClearMap/IO/TIF.py", line 234, in metadata
parser.parse()
File "/home/gangliaguardian/anaconda3/envs/ClearMapUi39/lib/python3.9/site-packages/ClearMap2-2.1.3-py3.9-linux-x86_64.egg/ClearMap/IO/TIF.py", line 301, in parse
self.parse_pixel_metadata()
File "/home/gangliaguardian/anaconda3/envs/ClearMapUi39/lib/python3.9/site-packages/ClearMap2-2.1.3-py3.9-linux-x86_64.egg/ClearMap/IO/TIF.py", line 346, in parse_pixel_metadata
self.parse_order()
File "/home/gangliaguardian/anaconda3/envs/ClearMapUi39/lib/python3.9/site-packages/ClearMap2-2.1.3-py3.9-linux-x86_64.egg/ClearMap/IO/TIF.py", line 471, in parse_order
super().parse_order()
File "/home/gangliaguardian/anaconda3/envs/ClearMapUi39/lib/python3.9/site-packages/ClearMap2-2.1.3-py3.9-linux-x86_64.egg/ClearMap/IO/TIF.py", line 327, in parse_order
self.info['order'] = self.pixels_metadata.get('DimensionOrder', None)
File "/home/gangliaguardian/anaconda3/envs/ClearMapUi39/lib/python3.9/functools.py", line 993, in get
val = self.func(instance)
File "/home/gangliaguardian/anaconda3/envs/ClearMapUi39/lib/python3.9/site-packages/ClearMap2-2.1.3-py3.9-linux-x86_64.egg/ClearMap/IO/TIF.py", line 374, in pixels_metadata
raise NotImplementedError("Subclasses should implement this method")
NotImplementedError: Subclasses should implement this method
Any help would be greatly appreciated!
The text was updated successfully, but these errors were encountered:
I am attempting to establish my sample in the ClearMap2 GUI, but I am running into an error after selecting my source folder, which contains two sub-folders each containing a sequence of tiff files for both the cFos and Autofluorescence channels respectively. We are unfortunately running into the following error log:
_WorkspaceCellMap{/home/gangliaguardian/Documents/clearmap2test}
directories:
[ data]: /home/gangliaguardian/Documents/clearmap2test
[analysis]: /home/gangliaguardian/Documents/clearmap2test
files:
[data ] raw : no file
[data ] autofluorescence : no file
[analysis] stitched : no file
[analysis] layout : no file
[analysis] background : no file
[data ] resampled : no file
[data ] autofluorescence_resampled : no file
[data ] resampled_to_autofluorescence : no file
[data ] resampled_aligned_to_autofluorescence: no file
[data ] autofluorescence_to_reference : no file
[data ] autofluorescence_aligned_to_reference: no file
[analysis] cells : no file
[analysis] density : no file
[analysis] tile_extension : no file
Preparing: '/home/gangliaguardian/anaconda3/envs/ClearMapUi39/lib/python3.9/site-packages/ClearMap2-2.1.3-py3.9-linux-x86_64.egg/ClearMap/Resources/Atlas/ABA_25um_2017_annotation_-1_2_3__slice_None_None_None__slice_None_None_None__slice_None_None_None__.tif'
Preparing: from source Tif-Source((320, 528, 456),)[uint32]/home/gangliaguardian/anaconda3/envs/ClearMapUi39/...arMap/Resources/Atlas/ABA_25um_2017_annotation.tif
Traceback (most recent call last):
File "/home/gangliaguardian/anaconda3/envs/ClearMapUi39/lib/python3.9/site-packages/ClearMap2-2.1.3-py3.9-linux-x86_64.egg/ClearMap/gui/run_gui.py", line 1133, in load_config_and_setup_ui
tab.setup_workers()
File "/home/gangliaguardian/anaconda3/envs/ClearMapUi39/lib/python3.9/site-packages/ClearMap2-2.1.3-py3.9-linux-x86_64.egg/ClearMap/gui/tabs.py", line 327, in setup_workers
self.wrap_step('Setting up atlas', self.setup_atlas, n_steps=1, save_cfg=False, nested=False) # TODO: abort_func=self.preprocessor.stop_process
File "/home/gangliaguardian/anaconda3/envs/ClearMapUi39/lib/python3.9/site-packages/ClearMap2-2.1.3-py3.9-linux-x86_64.egg/ClearMap/gui/interfaces.py", line 299, in wrap_step
self.main_window.wrap_in_thread(func, *step_args, **step_kw_args)
File "/home/gangliaguardian/anaconda3/envs/ClearMapUi39/lib/python3.9/site-packages/ClearMap2-2.1.3-py3.9-linux-x86_64.egg/ClearMap/gui/run_gui.py", line 629, in wrap_in_thread
return result.get()
File "/home/gangliaguardian/anaconda3/envs/ClearMapUi39/lib/python3.9/multiprocessing/pool.py", line 771, in get
raise self.value
File "/home/gangliaguardian/anaconda3/envs/ClearMapUi39/lib/python3.9/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, **kwds))
File "/home/gangliaguardian/anaconda3/envs/ClearMapUi39/lib/python3.9/site-packages/ClearMap2-2.1.3-py3.9-linux-x86_64.egg/ClearMap/gui/tabs.py", line 406, in setup_atlas
self.preprocessor.setup_atlases()
File "/home/gangliaguardian/anaconda3/envs/ClearMapUi39/lib/python3.9/site-packages/ClearMap2-2.1.3-py3.9-linux-x86_64.egg/ClearMap/processors/sample_preparation.py", line 366, in setup_atlases
res = annotation.prepare_annotation_files(
File "/home/gangliaguardian/anaconda3/envs/ClearMapUi39/lib/python3.9/site-packages/ClearMap2-2.1.3-py3.9-linux-x86_64.egg/ClearMap/Alignment/Annotation.py", line 744, in prepare_annotation_files
data = np.array(s.array)
File "/home/gangliaguardian/anaconda3/envs/ClearMapUi39/lib/python3.9/site-packages/ClearMap2-2.1.3-py3.9-linux-x86_64.egg/ClearMap/IO/TIF.py", line 128, in array
return self.to_clearmap_order(array)
File "/home/gangliaguardian/anaconda3/envs/ClearMapUi39/lib/python3.9/site-packages/ClearMap2-2.1.3-py3.9-linux-x86_64.egg/ClearMap/IO/TIF.py", line 173, in to_clearmap_order
transposed = tif_to_clearmap_order(array, self.axes_order)
File "/home/gangliaguardian/anaconda3/envs/ClearMapUi39/lib/python3.9/site-packages/ClearMap2-2.1.3-py3.9-linux-x86_64.egg/ClearMap/IO/TIF.py", line 66, in axes_order
md = self.metadata(info=['shape'])
File "/home/gangliaguardian/anaconda3/envs/ClearMapUi39/lib/python3.9/site-packages/ClearMap2-2.1.3-py3.9-linux-x86_64.egg/ClearMap/IO/TIF.py", line 234, in metadata
parser.parse()
File "/home/gangliaguardian/anaconda3/envs/ClearMapUi39/lib/python3.9/site-packages/ClearMap2-2.1.3-py3.9-linux-x86_64.egg/ClearMap/IO/TIF.py", line 301, in parse
self.parse_pixel_metadata()
File "/home/gangliaguardian/anaconda3/envs/ClearMapUi39/lib/python3.9/site-packages/ClearMap2-2.1.3-py3.9-linux-x86_64.egg/ClearMap/IO/TIF.py", line 346, in parse_pixel_metadata
self.parse_order()
File "/home/gangliaguardian/anaconda3/envs/ClearMapUi39/lib/python3.9/site-packages/ClearMap2-2.1.3-py3.9-linux-x86_64.egg/ClearMap/IO/TIF.py", line 471, in parse_order
super().parse_order()
File "/home/gangliaguardian/anaconda3/envs/ClearMapUi39/lib/python3.9/site-packages/ClearMap2-2.1.3-py3.9-linux-x86_64.egg/ClearMap/IO/TIF.py", line 327, in parse_order
self.info['order'] = self.pixels_metadata.get('DimensionOrder', None)
File "/home/gangliaguardian/anaconda3/envs/ClearMapUi39/lib/python3.9/functools.py", line 993, in get
val = self.func(instance)
File "/home/gangliaguardian/anaconda3/envs/ClearMapUi39/lib/python3.9/site-packages/ClearMap2-2.1.3-py3.9-linux-x86_64.egg/ClearMap/IO/TIF.py", line 374, in pixels_metadata
raise NotImplementedError("Subclasses should implement this method")
NotImplementedError: Subclasses should implement this method
Any help would be greatly appreciated!
The text was updated successfully, but these errors were encountered: